Cell Phase

Creature Phase

Tribal Phase

Civilization Phase

Space Phase

The space phase involves players spreading their creature population throughout the universe as they complete mission-type goals. This includes acquiring tools to terraform otherwise uninhabitable planets. The ultimate tool for this purpose is a technology which Wright dubbed the Genesis device, named after the device in Star Trek II: The Wrath of Khan, both of which have the same purpose: transform a dead world into a planet capable of sustaining life in a matter of minutes. During the 2007 TED conference, Wright showed off the planetary effects the UFO can have, such as pumping carbon dioxide into the atmosphere to increase the amount of greenhouse gases, which over time caused the oceans initially to rise and flood coastal cities, then eventually evaporate and transform the world into an arid desert planet, followed by a molten rock in space. Wright semi-jokingly called it "a sequel to An Inconvenient Truth." The player may cause icy comets to crash into a planet to create water, or force volcanoes to erupt to increase atmosphere. Players may build cities underwater or on the surface of an inhospitable planet once they gain the ability to create bubbled cities, similar in function to self-sustaining arcologies. Once the world around them becomes habitable, the city loses the bubble.

During exploration of other worlds, the player may scan content and add the information to a database designed like a trading card deck called the Sporepedia. The player may also abduct creatures and transport them to other planets to test a planet's habitability. The player may interbreed different species genetically, or place a monolith (in the style of 2001: A Space Odyssey) on a planet, triggering evolution of intelligent life, then come back later to see what has evolved. On lifeless worlds, the player may also find strange "artifacts" with unknown purposes to be used later on, possibly adding tools for the UFO.

Once the player has explored neighboring worlds, interstellar travel becomes possible. There are more than 4 billion planets in the game's galaxy, more than anyone can visit in a lifetime. During the 2007 TED Conference seminar, Wright used accelerated time dilation in the zoomed-out galaxy view to show the dynamics of the entire galaxy, as supernovae exploded in brilliant points of light, and the galactic arms slowly turned. He pointed out that the nebulae, which the game features in real-life separate categories of planetary nebulae and reflection nebulae, perform their actual functions in space. He also brought the UFO close to a black hole, keeping a cautionary distance from the gravitational singularity.

Players can make contact with other civilizations, most of which are created by other players. Intelligent species can be found by running the mouse over other star systems and their individual planets to try to pick up radio static or noise that can indicate intelligent life. When the UFO visits that world, they may impress the beings with fireworks, attack them with weapons, or try to establish a language with the civilization via a Close Encounters of the Third Kind-styled musical mini-game. The player may beam down a holographic image of his/her creature to interact more directly with an alien species. A user-created civilization's AI reacts depending on its behavior and personality, both of which are based on the play-style of its user. The player can unite or conquer the galaxy by diplomatically creating a federation or sparking an interstellar war. As a show of great force, the player may even use a weapon to completely destroy a planet (similar to the capabilities of the Death Star from the Star Wars saga), which will sometimes bring retribution from that species and its allies. The player is sometimes called upon to fight off an invasion of their home planet.

Currency, as with the civilization phase, is Spice.

Sandbox

The space phase is sometimes referred to as a sandbox, because the player has near-complete control of everything. It has been mentioned that the space phase works on two axes: a horizontal axis (the ability to interact with many planets in a variety of different ways) and a vertical axis (the ability to revisit different phases of gameplay).